Comparing OTUs from different V regions?

[JenBarb]

Hello,
I have data generated from using 6 different primers which target 6 different V regions of the 16s gene from the same samples. I am wondering if anyone has any advice on how to compare or combine the results from the different regions in order to come up with a consensus result?

I know that this is a tricky question but I am just curious if anyone else is doign this and what advice they might have for this.
Thanks,
Jen

[thermophile]

the only way to compare across regions is to just taxonomically identify the sequences against the same database and compare the results. Depending on what your samples are and how well your organisms are represented in the databases, the results could be between mildly interesting and a waste of time. (I tried something like this on 454 sequenced deep ocean samples v8-9 vs v1-3, it was a waste of time). If you are trying to determine what region to use for a larger study, you're better off creating a database of full length sequences that are representative of your communities and doing the comparison in silico